Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014051.1 Corchorus capsularis cultivar CVL-1 contig14072, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 136671
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:587 original size:31 final size:29
Alignment explanation
Indices: 521--600 Score: 106
Period size: 29 Copynumber: 2.7 Consensus size: 29
511 CTCATTTTTG
* * *
521 AAACGTAAGGGATTAATTTGTCCCGAAAA
1 AAACATAAGGGATTATTTTGTCCCAAAAA
550 AAACATAAGGGATTATTTTGTCCCAAAAGCA
1 AAACATAAGGGATTATTTTGTCCCAAAA--A
*
581 AAACATAAGGGATTTTTTTG
1 AAACATAAGGGATTATTTTG
601 GGTATTTAGC
Statistics
Matches: 45, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
29 25 0.56
31 20 0.44
ACGTcount: A:0.40, C:0.12, G:0.19, T:0.29
Consensus pattern (29 bp):
AAACATAAGGGATTATTTTGTCCCAAAAA
Found at i:3366 original size:440 final size:439
Alignment explanation
Indices: 2530--3476 Score: 1414
Period size: 440 Copynumber: 2.2 Consensus size: 439
2520 GTAAAGGATG
** * * *
2530 AAATAGCATAAAAACATAAAAGTATGAGGATCATTTGATAAATAATCCAGCAAGAGAAATATTTG
1 AAATAGCAT-AAATTATAAAAGTATAAGGATCATTTGATAAATAATCCAGCAAAAAAAAT-TTTG
* *
2595 TTTATGGAGACCAAACATAAAAATCAATTCTCAAACTCTCCACGAAACTCATTAATCAAATCCAG
64 TTTACGGAGACCAAACATAAAAATCAATTCTCAAACCCTCCACGAAACTCATTAATCAAATCCAG
* * * *
2660 CTTTCAAACCCTTAACGAAAGTCATAGATCACACAATAACCTTTTAACCGACACTTGAGCAATCT
129 CTTTCAAACCCTTAACGAAAATCATAGATCACAAAATAACCTTTTAACCGACACTTGAACAACCT
* * * * *
2725 CAATCGGACAAGTGGACTGAAACTTATACAATATTAGATAGACCGGCAATCGAGAGCACAAAATT
194 CAATCGAACAAGTAGACCGAAACTTATACAATATTAGATAGACCGACAATCGAGACCACAAAATT
* * * * * *
2790 TCAGAAGTATTTTTTAGAATCAGAACATTAACATTGGCTTTTGAGTCCTTCATGGAAGTTGTGGA
259 TCAGAAGCATTTTTTAGAATCAAAACATTAAAATTGGCTTTCGAGTCCTTCATGGAAGTTATAGA
** * *
2855 TCATGATTTTACCTTTTAATAGACACTTAAATCACCTTGATCGGACAAGCAAAAGAAAAAATAAA
324 TCATGAAATTACATTTTAATAGACACTTAAATCACCTTGATCGGACAAGCAAAACAAAAAATAAA
* * *
2920 AGAATTAAAGTCGAAACGTTCAATCGTCCAACCCAAAATTTGTGATGGACT
389 AGAATTAAAGCCGAAACATTCAATCATCCAACCCAAAATTTGTGATGGACT
2971 AAATAGCATAAATTATAAAAGTATAAGGATCATTTTGATAAATAATCCAGCAAAAAAAATTTTGT
1 AAATAGCATAAATTATAAAAGTATAAGGATCA-TTTGATAAATAATCCAGCAAAAAAAATTTTGT
** *
3036 TTACGGAGACCAAACATAAAAATTC-ATTCTTGAACCCTCCACGAAATTCATTAATCAAATCCAG
65 TTACGGAGACCAAACATAAAAA-TCAATTCTCAAACCCTCCACGAAACTCATTAATCAAATCCAG
* * *
3100 CTTTCAGACCCTTAAGGAAAATCGTAGATCACAAAATAACCTTTTAACCGACACTTGAACAACCT
129 CTTTCAAACCCTTAACGAAAATCATAGATCACAAAATAACCTTTTAACCGACACTTGAACAACCT
* * *
3165 CAATCGAAGAAGTAGACCGAAACTTATACAGTATTAGATAGACCGACAATTGAGACCACAAAATT
194 CAATCGAACAAGTAGACCGAAACTTATACAATATTAGATAGACCGACAATCGAGACCACAAAATT
3230 TCAGAAGCATTTTTTAGAATCAAAACATTAAAATTGGCTTTCGAGTCCTTCATGGAAGTTATAGA
259 TCAGAAGCATTTTTTAGAATCAAAACATTAAAATTGGCTTTCGAGTCCTTCATGGAAGTTATAGA
* * *
3295 TCATGAAATTACATTTTAATAGACACTTGAATCACCTTGATCGGACAAGTAAAACAAAAGATAAA
324 TCATGAAATTACATTTTAATAGACACTTAAATCACCTTGATCGGACAAGCAAAACAAAAAATAAA
*
3360 AGAATTAAAGCCGAAACATTCAATCATCCAACCCAGAATTTGTGATGGACT
389 AGAATTAAAGCCGAAACATTCAATCATCCAACCCAAAATTTGTGATGGACT
* * * *
3411 AAATAACATAAATTATAAAAGTATAGGGACCATTTGAT-AATCAATCCAGC-AAAAAATTTTTGT
1 AAATAGCATAAATTATAAAAGTATAAGGATCATTTGATAAAT-AATCCAGCAAAAAAAATTTTGT
3474 TTA
65 TTA
3477 TTGAGAGCGG
Statistics
Matches: 457, Mismatches: 46, Indels: 9
0.89 0.09 0.02
Matches are distributed among these distances:
438 18 0.04
439 14 0.03
440 389 0.85
441 36 0.08
ACGTcount: A:0.42, C:0.18, G:0.14, T:0.27
Consensus pattern (439 bp):
AAATAGCATAAATTATAAAAGTATAAGGATCATTTGATAAATAATCCAGCAAAAAAAATTTTGTT
TACGGAGACCAAACATAAAAATCAATTCTCAAACCCTCCACGAAACTCATTAATCAAATCCAGCT
TTCAAACCCTTAACGAAAATCATAGATCACAAAATAACCTTTTAACCGACACTTGAACAACCTCA
ATCGAACAAGTAGACCGAAACTTATACAATATTAGATAGACCGACAATCGAGACCACAAAATTTC
AGAAGCATTTTTTAGAATCAAAACATTAAAATTGGCTTTCGAGTCCTTCATGGAAGTTATAGATC
ATGAAATTACATTTTAATAGACACTTAAATCACCTTGATCGGACAAGCAAAACAAAAAATAAAAG
AATTAAAGCCGAAACATTCAATCATCCAACCCAAAATTTGTGATGGACT
Found at i:4019 original size:29 final size:29
Alignment explanation
Indices: 3962--4019 Score: 89
Period size: 29 Copynumber: 2.0 Consensus size: 29
3952 TCCCCTCTAA
*
3962 TATAGCTACTATCCAATGATTTCCAATAT
1 TATAGCTACTATCCAATGATTTACAATAT
* *
3991 TATAGCTAGTATCCAATGATTTACTATAT
1 TATAGCTACTATCCAATGATTTACAATAT
4020 AGTGTTGGAT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.34, C:0.17, G:0.09, T:0.40
Consensus pattern (29 bp):
TATAGCTACTATCCAATGATTTACAATAT
Found at i:4228 original size:4 final size:4
Alignment explanation
Indices: 4219--4254 Score: 63
Period size: 4 Copynumber: 9.0 Consensus size: 4
4209 GAAGAAGAAG
*
4219 AAAC AAAC AAAC AAAC AAAC AAAC AACC AAAC AAAC
1 AAAC AAAC AAAC AAAC AAAC AAAC AAAC AAAC AAAC
4255 TGGACAAAGG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
4 30 1.00
ACGTcount: A:0.72, C:0.28, G:0.00, T:0.00
Consensus pattern (4 bp):
AAAC
Found at i:6324 original size:12 final size:11
Alignment explanation
Indices: 6307--6350 Score: 63
Period size: 11 Copynumber: 3.9 Consensus size: 11
6297 TCTAAATGAT
6307 TTTTTCTTTTTC
1 TTTTT-TTTTTC
6319 TTTTTCTTTTTC
1 TTTTT-TTTTTC
6331 -TTTTTTTTTC
1 TTTTTTTTTTC
6341 TTTTTTTTTT
1 TTTTTTTTTT
6351 TTGTCTACTA
Statistics
Matches: 31, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
10 6 0.19
11 13 0.42
12 12 0.39
ACGTcount: A:0.00, C:0.11, G:0.00, T:0.89
Consensus pattern (11 bp):
TTTTTTTTTTC
Found at i:6352 original size:6 final size:6
Alignment explanation
Indices: 6307--6350 Score: 67
Period size: 6 Copynumber: 7.8 Consensus size: 6
6297 TCTAAATGAT
6307 TTTTTC TTTTTC TTTTTC TTTTTC -TTTT- TTTTTC TTTTT- TTTTT
1 TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC TTTTT
6351 TTGTCTACTA
Statistics
Matches: 36, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
5 13 0.36
6 23 0.64
ACGTcount: A:0.00, C:0.11, G:0.00, T:0.89
Consensus pattern (6 bp):
TTTTTC
Found at i:6870 original size:24 final size:24
Alignment explanation
Indices: 6843--6891 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
6833 CTTTCGTTTC
6843 AATCTCAAACTTGCCCTAGTCAGT
1 AATCTCAAACTTGCCCTAGTCAGT
6867 AATCTCAAACTTGCCCTAGTCAGT
1 AATCTCAAACTTGCCCTAGTCAGT
6891 A
1 A
6892 CAACATAGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.31, C:0.29, G:0.12, T:0.29
Consensus pattern (24 bp):
AATCTCAAACTTGCCCTAGTCAGT
Found at i:7679 original size:9 final size:9
Alignment explanation
Indices: 7665--7689 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
7655 CTTTGCAAGG
7665 ATCCAGGAC
1 ATCCAGGAC
7674 ATCCAGGAC
1 ATCCAGGAC
7683 ATCCAGG
1 ATCCAGG
7690 TCTTTCTAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.32, C:0.32, G:0.24, T:0.12
Consensus pattern (9 bp):
ATCCAGGAC
Found at i:12312 original size:30 final size:30
Alignment explanation
Indices: 12276--12340 Score: 87
Period size: 30 Copynumber: 2.2 Consensus size: 30
12266 CCCTGGACTT
*
12276 CCTCTCCCTTTC-CTTCTCCTTTTCCCTCTC
1 CCTCTCCCTTTCTCTT-TCCCTTTCCCTCTC
* *
12306 CCTCTCCCTTTCTCTTTCCCTTTCTCTTTC
1 CCTCTCCCTTTCTCTTTCCCTTTCCCTCTC
12336 CCTCT
1 CCTCT
12341 TTTCTCGCTC
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
30 28 0.90
31 3 0.10
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (30 bp):
CCTCTCCCTTTCTCTTTCCCTTTCCCTCTC
Found at i:12364 original size:12 final size:12
Alignment explanation
Indices: 12276--12374 Score: 74
Period size: 12 Copynumber: 8.0 Consensus size: 12
12266 CCCTGGACTT
*
12276 CCTCTCCCTTTC
1 CCTCTCTCTTTC
*
12288 CTTCTC-CTTTTC
1 CCTCTCTC-TTTC
* *
12300 CCTCTCCCTCTC
1 CCTCTCTCTTTC
*
12312 CCTTTCTCTTTC
1 CCTCTCTCTTTC
*
12324 CCTTTCTCTTTC
1 CCTCTCTCTTTC
**
12336 CCTCTTTTCTCGCTC
1 CCTC---TCTCTTTC
12351 CCTCTCTCTTTC
1 CCTCTCTCTTTC
*
12363 CCTTTCTCTTTC
1 CCTCTCTCTTTC
12375 ACGCTTCTCC
Statistics
Matches: 70, Mismatches: 12, Indels: 10
0.76 0.13 0.11
Matches are distributed among these distances:
11 1 0.01
12 58 0.83
13 1 0.01
15 10 0.14
ACGTcount: A:0.00, C:0.48, G:0.01, T:0.51
Consensus pattern (12 bp):
CCTCTCTCTTTC
Found at i:12402 original size:6 final size:6
Alignment explanation
Indices: 12280--12338 Score: 57
Period size: 6 Copynumber: 9.8 Consensus size: 6
12270 GGACTTCCTC
* * * *
12280 TCCCTT T-CCTT CTCCTTT TCCCTC TCCCTC TCCCTT TCTCTT TCCCTT
1 TCCCTT TCCCTT -TCCCTT TCCCTT TCCCTT TCCCTT TCCCTT TCCCTT
*
12328 TCTCTT TCCCT
1 TCCCTT TCCCT
12339 CTTTTCTCGC
Statistics
Matches: 43, Mismatches: 8, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
5 4 0.09
6 36 0.84
7 3 0.07
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (6 bp):
TCCCTT
Found at i:12544 original size:75 final size:75
Alignment explanation
Indices: 12463--12620 Score: 190
Period size: 75 Copynumber: 2.1 Consensus size: 75
12453 CCTTTCCTTT
* * * * * *
12463 TCCCTATCTGAATCACTGCTCTTCTCCCTCTCAGAACGACGCCTTTCTCGTTCTCGTTCTCGATC
1 TCCCTATCGGAATCACTGCTCCTCTCCCTCTCAGAACGACGCCGTTCACGCTCCCGTTCTCGATC
12528 CCTATCCCTA
66 CCTATCCCTA
* * * * *
12538 TCCCTATCGGAGTCACTGCTCCTCTCTCTCTCGGAACGGCGTCGTTCACGCTCCCGTTCTCGATC
1 TCCCTATCGGAATCACTGCTCCTCTCCCTCTCAGAACGACGCCGTTCACGCTCCCGTTCTCGATC
* * *
12603 TCTTTCTCTA
66 CCTATCCCTA
12613 TCCCTATC
1 TCCCTATC
12621 CCTATCCCTA
Statistics
Matches: 69, Mismatches: 14, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
75 69 1.00
ACGTcount: A:0.13, C:0.40, G:0.13, T:0.34
Consensus pattern (75 bp):
TCCCTATCGGAATCACTGCTCCTCTCCCTCTCAGAACGACGCCGTTCACGCTCCCGTTCTCGATC
CCTATCCCTA
Found at i:18291 original size:6 final size:6
Alignment explanation
Indices: 18260--18318 Score: 55
Period size: 6 Copynumber: 9.8 Consensus size: 6
18250 CCCTGGACTT
* * * * *
18260 CCTCTC CCTTTC CTTCTC CTTTTC CCTCTC CCTCTC CCTCTC CCTTTC
1 CCTCTC CCTCTC CCTCTC CCTCTC CCTCTC CCTCTC CCTCTC CCTCTC
* *
18308 TCTTTC CCTCT
1 CCTCTC CCTCT
18319 TTTCTCGCTC
Statistics
Matches: 43, Mismatches: 10, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
6 43 1.00
ACGTcount: A:0.00, C:0.54, G:0.00, T:0.46
Consensus pattern (6 bp):
CCTCTC
Found at i:18292 original size:24 final size:24
Alignment explanation
Indices: 18260--18318 Score: 73
Period size: 24 Copynumber: 2.5 Consensus size: 24
18250 CCCTGGACTT
* * *
18260 CCTCTCCCTTTCCTTCTCCTTTTC
1 CCTCTCCCTCTCCCTCTCCCTTTC
18284 CCTCTCCCTCTCCCTCTCCCTTTC
1 CCTCTCCCTCTCCCTCTCCCTTTC
* *
18308 TCTTTCCCTCT
1 CCTCTCCCTCT
18319 TTTCTCGCTC
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.00, C:0.54, G:0.00, T:0.46
Consensus pattern (24 bp):
CCTCTCCCTCTCCCTCTCCCTTTC
Found at i:18363 original size:33 final size:32
Alignment explanation
Indices: 18292--18379 Score: 81
Period size: 33 Copynumber: 2.7 Consensus size: 32
18282 TCCCTCTCCC
* *
18292 TCTCCCTCTCCCTTTCTCTTTCCCTCTTTTCTCG
1 TCTCCCTCTCTCTTTCTCTTT--CTCTTTTCACG
18326 -CTCCCTCTCTCTTTCTCTTTCTC-TTTCACG
1 TCTCCCTCTCTCTTTCTCTTTCTCTTTTCACG
** *
18356 CTTCTCCCTAGCTCTTTCCCTTTC
1 --TCTCCCTCTCTCTTTCTCTTTC
18380 CTTCTCTTTC
Statistics
Matches: 46, Mismatches: 5, Indels: 7
0.79 0.09 0.12
Matches are distributed among these distances:
30 6 0.13
31 3 0.07
33 37 0.80
ACGTcount: A:0.02, C:0.45, G:0.03, T:0.49
Consensus pattern (32 bp):
TCTCCCTCTCTCTTTCTCTTTCTCTTTTCACG
Found at i:34362 original size:30 final size:30
Alignment explanation
Indices: 34328--34384 Score: 105
Period size: 30 Copynumber: 1.9 Consensus size: 30
34318 TTAGTGATTC
34328 TGAGACCGACAATGCTAGTGATGATGACTT
1 TGAGACCGACAATGCTAGTGATGATGACTT
*
34358 TGAGAGCGACAATGCTAGTGATGATGA
1 TGAGACCGACAATGCTAGTGATGATGA
34385 AGATTTCTAA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.32, C:0.14, G:0.30, T:0.25
Consensus pattern (30 bp):
TGAGACCGACAATGCTAGTGATGATGACTT
Found at i:34658 original size:20 final size:21
Alignment explanation
Indices: 34620--34659 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
34610 ATGTTTGCAG
*
34620 TCACTTCTCTTTGAATCTCAC
1 TCACTTCTCTTGGAATCTCAC
*
34641 TCACTT-TCTTGGATTCTCA
1 TCACTTCTCTTGGAATCTCA
34660 AAAACAAGCG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.17, C:0.30, G:0.07, T:0.45
Consensus pattern (21 bp):
TCACTTCTCTTGGAATCTCAC
Found at i:35537 original size:10 final size:10
Alignment explanation
Indices: 35512--35550 Score: 53
Period size: 10 Copynumber: 3.9 Consensus size: 10
35502 GGGCCATACC
35512 TAAAATATAAA
1 TAAAAT-TAAA
35523 T-AAATTAAA
1 TAAAATTAAA
35532 TAAAATTAAA
1 TAAAATTAAA
*
35542 TTAAATTAA
1 TAAAATTAA
35551 TCGTGGCATT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
9 5 0.19
10 20 0.77
11 1 0.04
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (10 bp):
TAAAATTAAA
Found at i:35541 original size:15 final size:15
Alignment explanation
Indices: 35514--35547 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
35504 GCCATACCTA
35514 AAATATAAATAAATT
1 AAATATAAATAAATT
35529 AAATA-AAATTAAATT
1 AAATATAAA-TAAATT
35544 AAAT
1 AAAT
35548 TAATCGTGGC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 3 0.17
15 15 0.83
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (15 bp):
AAATATAAATAAATT
Found at i:43431 original size:26 final size:27
Alignment explanation
Indices: 43374--43431 Score: 82
Period size: 27 Copynumber: 2.2 Consensus size: 27
43364 AAGAAAAATT
***
43374 AAAGTTTTATTTTCTTCTGGCCAAAAA
1 AAAGTTTTATTTTCTTCTCAACAAAAA
43401 AAAGTTTTATTTTCTTC-CAACAAAAA
1 AAAGTTTTATTTTCTTCTCAACAAAAA
43427 AAAGT
1 AAAGT
43432 AATTTTTCTT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
26 11 0.39
27 17 0.61
ACGTcount: A:0.40, C:0.14, G:0.09, T:0.38
Consensus pattern (27 bp):
AAAGTTTTATTTTCTTCTCAACAAAAA
Found at i:53029 original size:2 final size:2
Alignment explanation
Indices: 53022--53049 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
53012 ACACGATTAA
53022 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
53050 GTGTGTGTGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:55804 original size:33 final size:33
Alignment explanation
Indices: 55762--55858 Score: 146
Period size: 30 Copynumber: 3.0 Consensus size: 33
55752 CCTTGCTCTT
55762 CCTTGGATACTTCTTCCTTGCTTTCTCCATTTA
1 CCTTGGATACTTCTTCCTTGCTTTCTCCATTTA
**
55795 CCTTGGATACTTCTTCCTT-AATT-T-CATTTA
1 CCTTGGATACTTCTTCCTTGCTTTCTCCATTTA
*
55825 CCTTGGATACTTCTTCCTTGCTTTCTCCGTTTA
1 CCTTGGATACTTCTTCCTTGCTTTCTCCATTTA
55858 C
1 C
55859 TGGAGTAGGT
Statistics
Matches: 56, Mismatches: 5, Indels: 6
0.84 0.07 0.09
Matches are distributed among these distances:
30 25 0.45
31 3 0.05
32 3 0.05
33 25 0.45
ACGTcount: A:0.13, C:0.29, G:0.09, T:0.48
Consensus pattern (33 bp):
CCTTGGATACTTCTTCCTTGCTTTCTCCATTTA
Found at i:57616 original size:21 final size:21
Alignment explanation
Indices: 57575--57618 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
57565 GTTGAAGGAT
* *
57575 TATTATTATTATATTATTATA
1 TATTATTATAATATTAATATA
57596 TATTATTATAATGA-TAATATA
1 TATTATTATAAT-ATTAATATA
57617 TA
1 TA
57619 CTGTTGCTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 19 0.95
22 1 0.05
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (21 bp):
TATTATTATAATATTAATATA
Found at i:59871 original size:5 final size:5
Alignment explanation
Indices: 59850--59884 Score: 52
Period size: 5 Copynumber: 6.8 Consensus size: 5
59840 TGCTTATAAG
*
59850 TTTTT TTTTA TTATTA TTTTA TTTTA TTTTA TTTT
1 TTTTA TTTTA TT-TTA TTTTA TTTTA TTTTA TTTT
59885 TTTGTTGGCA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
5 23 0.82
6 5 0.18
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (5 bp):
TTTTA
Found at i:59885 original size:16 final size:16
Alignment explanation
Indices: 59850--59887 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
59840 TGCTTATAAG
59850 TTTTTTTTTATTATTA
1 TTTTTTTTTATTATTA
*
59866 TTTTATTTTATT-TTA
1 TTTTTTTTTATTATTA
59881 TTTTTTT
1 TTTTTTT
59888 GTTGGCATAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
15 9 0.45
16 11 0.55
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (16 bp):
TTTTTTTTTATTATTA
Found at i:62244 original size:18 final size:18
Alignment explanation
Indices: 62223--62259 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
62213 TAGGTGGAAG
62223 ATCAGTTATGGAGATAAA
1 ATCAGTTATGGAGATAAA
*
62241 ATCAGTTATGGATATAAA
1 ATCAGTTATGGAGATAAA
62259 A
1 A
62260 AAACAAACAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.46, C:0.05, G:0.19, T:0.30
Consensus pattern (18 bp):
ATCAGTTATGGAGATAAA
Found at i:67719 original size:160 final size:164
Alignment explanation
Indices: 67507--67824 Score: 486
Period size: 163 Copynumber: 2.0 Consensus size: 164
67497 ACATATTATG
67507 ATTCTTGAATAACACTAATTTGGCATAGAGATTTTAATTGAAGGAATATATACTGT-TGCTAATA
1 ATTCTTGAATAACACTAATTTGGCATA-AGATTTTAATTGAAGGAATATATACTGTAT-CTAATA
*
67571 AAAATG-AAAGAAAATCAAATTGG-CC-T-TACTAACTAAAACACAGACAGAAAGATTTGACAAT
64 AAAAAGAAAAGAAAATCAAA-TGGACCTTATACTAACTAAAACACAGACAGAAAGATTTGACAAT
*
67632 AAACAATTAATTCGGAGAGTTATTAAAAATGATAGTA
128 AAACAAATAATTCGGAGAGTTATTAAAAATGATAGTA
* * *
67669 ATTCTTGATTAACACTAATTTGGCCT-AGATTTTAATTGAAGGATTATATACTGTATCTAATAAA
1 ATTCTTGAATAACACTAATTTGGCATAAGATTTTAATTGAAGGAATATATACTGTATCTAATAAA
* * *
67733 AAAGAAAAGAAAATCTAATGGACCTTATAGTAACTAAAACACAGACAGAAAGATTTGTCAATAAA
66 AAAGAAAAGAAAATCAAATGGACCTTATACTAACTAAAACACAGACAGAAAGATTTGACAATAAA
*
67798 CAAATAATTCGGGGAGTTATTAAAAAT
131 CAAATAATTCGGAGAGTTATTAAAAAT
67825 AGAAAAAAGA
Statistics
Matches: 142, Mismatches: 9, Indels: 9
0.89 0.06 0.06
Matches are distributed among these distances:
160 41 0.29
161 15 0.11
162 25 0.18
163 61 0.43
ACGTcount: A:0.45, C:0.11, G:0.14, T:0.30
Consensus pattern (164 bp):
ATTCTTGAATAACACTAATTTGGCATAAGATTTTAATTGAAGGAATATATACTGTATCTAATAAA
AAAGAAAAGAAAATCAAATGGACCTTATACTAACTAAAACACAGACAGAAAGATTTGACAATAAA
CAAATAATTCGGAGAGTTATTAAAAATGATAGTA
Found at i:74215 original size:6 final size:6
Alignment explanation
Indices: 74206--74248 Score: 61
Period size: 6 Copynumber: 7.2 Consensus size: 6
74196 AAGGAAAAGA
*
74206 AGAAGC AGAAGC AGAAGC AGAAGC AGAA-C AAGAAGC AAAAGC A
1 AGAAGC AGAAGC AGAAGC AGAAGC AGAAGC -AGAAGC AGAAGC A
74249 TCAGCACCCA
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
5 1 0.03
6 32 0.94
7 1 0.03
ACGTcount: A:0.56, C:0.16, G:0.28, T:0.00
Consensus pattern (6 bp):
AGAAGC
Found at i:85575 original size:30 final size:31
Alignment explanation
Indices: 85516--85580 Score: 87
Period size: 30 Copynumber: 2.1 Consensus size: 31
85506 AACTTTATGT
* * **
85516 TTTCCGATTGTACCCTTATTTTTAAAACATA
1 TTTCCAATTGTACACTTATTTAAAAAACATA
85547 TTTCCAATTGTACACTT-TTTAAAAAACATA
1 TTTCCAATTGTACACTTATTTAAAAAACATA
85577 TTTC
1 TTTC
85581 TAAATTACCA
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
30 15 0.50
31 15 0.50
ACGTcount: A:0.32, C:0.18, G:0.05, T:0.45
Consensus pattern (31 bp):
TTTCCAATTGTACACTTATTTAAAAAACATA
Found at i:87100 original size:66 final size:65
Alignment explanation
Indices: 86994--87145 Score: 191
Period size: 66 Copynumber: 2.3 Consensus size: 65
86984 CTTGTCTCTA
** * *
86994 TGTGGTTATCAAAATTTCATAAGATGGTTATTATAATTTCATGAG-GAT-GTTATCAAAATTCCA
1 TGTGGTTATCAAAATTTCATAAGAAAGTTATCAAAATTTCAT-AGTG-TGGTTA-CAAAATTCCA
87057 TAG
63 TAG
* * *
87060 TGTGGTTACCAAAATTTCATATGAAAGTTATCAAAATTTCATAGTGTGGTTACAAAATTTCATAG
1 TGTGGTTATCAAAATTTCATAAGAAAGTTATCAAAATTTCATAGTGTGGTTACAAAATTCCATAG
*
87125 TGTAGTTATCAAAATTTCATA
1 TGTGGTTATCAAAATTTCATA
87146 GGATCAGGTT
Statistics
Matches: 75, Mismatches: 9, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
65 34 0.45
66 41 0.55
ACGTcount: A:0.36, C:0.10, G:0.15, T:0.39
Consensus pattern (65 bp):
TGTGGTTATCAAAATTTCATAAGAAAGTTATCAAAATTTCATAGTGTGGTTACAAAATTCCATAG
Found at i:87132 original size:43 final size:43
Alignment explanation
Indices: 86998--87146 Score: 171
Period size: 44 Copynumber: 3.4 Consensus size: 43
86988 TCTCTATGTG
* ** *
86998 GTTATCAAAATTTCATAAG-ATGGTTATTATAATTTCATGAG-GA
1 GTTATCAAAATTTCAT-AGTGTGGTTACCAAAATTTCAT-AGTGA
*
87041 TGTTATCAAAATTCCATAGTGTGGTTACCAAAATTTCATA-TGAAA
1 -GTTATCAAAATTTCATAGTGTGGTTACCAAAATTTCATAGTG--A
87086 GTTATCAAAATTTCATAGTGTGGTTA-CAAAATTTCATAGTGTA
1 GTTATCAAAATTTCATAGTGTGGTTACCAAAATTTCATAGTG-A
87129 GTTATCAAAATTTCATAG
1 GTTATCAAAATTTCATAG
87147 GATCAGGTTA
Statistics
Matches: 93, Mismatches: 7, Indels: 11
0.84 0.06 0.10
Matches are distributed among these distances:
43 35 0.38
44 57 0.61
45 1 0.01
ACGTcount: A:0.37, C:0.10, G:0.15, T:0.38
Consensus pattern (43 bp):
GTTATCAAAATTTCATAGTGTGGTTACCAAAATTTCATAGTGA
Found at i:87193 original size:22 final size:23
Alignment explanation
Indices: 86994--87193 Score: 150
Period size: 22 Copynumber: 9.0 Consensus size: 23
86984 CTTGTCTCTA
*
86994 TGTGGTTATCAAAATTTCATAAG
1 TGTGGTTATCAAAATTTCATAGG
* * *
87017 -ATGGTTATTATAATTTCATGAGG
1 TGTGGTTATCAAAATTTCAT-AGG
* *
87040 -AT-GTTATCAAAATTCCATA-G
1 TGTGGTTATCAAAATTTCATAGG
*
87060 TGTGGTTACCAAAATTTCATA--
1 TGTGGTTATCAAAATTTCATAGG
**
87081 TGAAAGTTATCAAAATTTCATA-G
1 TG-TGGTTATCAAAATTTCATAGG
87104 TGTGGTTA-CAAAATTTCATA-G
1 TGTGGTTATCAAAATTTCATAGG
*
87125 TGTAGTTATCAAAATTTCATAGG
1 TGTGGTTATCAAAATTTCATAGG
** * * *
87148 ATCAGGTTATTAAAACTTCTTAGG
1 -TGTGGTTATCAAAATTTCATAGG
**
87172 T-TGGTTATTGAAATTTCATAGG
1 TGTGGTTATCAAAATTTCATAGG
87194 GTAGTTAATT
Statistics
Matches: 143, Mismatches: 26, Indels: 17
0.77 0.14 0.09
Matches are distributed among these distances:
20 1 0.01
21 24 0.17
22 93 0.65
23 8 0.06
24 17 0.12
ACGTcount: A:0.34, C:0.10, G:0.17, T:0.39
Consensus pattern (23 bp):
TGTGGTTATCAAAATTTCATAGG
Found at i:87261 original size:22 final size:22
Alignment explanation
Indices: 87236--87375 Score: 105
Period size: 22 Copynumber: 6.4 Consensus size: 22
87226 ATCAAAAAGA
*
87236 TTATCAAAATGTCATAGTGAGG
1 TTATCAAAATTTCATAGTGAGG
87258 TTAT-AAGAATTTCATAGT-ATGG
1 TTATCAA-AATTTCATAGTGA-GG
*
87280 TTAACAAAATTTCATTAG-GAGG
1 TTATCAAAATTTCA-TAGTGAGG
* * *
87302 TTA-CTAATATTTCATGGGGAGG
1 TTATC-AAAATTTCATAGTGAGG
**
87324 TTATCAAAAATTT-ATAGTCTGG
1 TTATC-AAAATTTCATAGTGAGG
*
87346 TTATCAAAATTTTATA-TGAAGG
1 TTATCAAAATTTCATAGTG-AGG
87368 TTAT-AAAA
1 TTATCAAAA
87376 GTCTCAATTT
Statistics
Matches: 96, Mismatches: 12, Indels: 21
0.74 0.09 0.16
Matches are distributed among these distances:
21 18 0.19
22 65 0.68
23 13 0.14
ACGTcount: A:0.38, C:0.07, G:0.18, T:0.37
Consensus pattern (22 bp):
TTATCAAAATTTCATAGTGAGG
Found at i:87468 original size:25 final size:22
Alignment explanation
Indices: 87433--87494 Score: 72
Period size: 21 Copynumber: 2.7 Consensus size: 22
87423 TCTCAGAATG
*
87433 ATTATCGAAATTTCATAGAGATCAA
1 ATTATCAAAATTTCATAG-GA--AA
*
87458 ATTATCAAAATTT-ATAGGAAG
1 ATTATCAAAATTTCATAGGAAA
87479 ATTATCAAAATTTCAT
1 ATTATCAAAATTTCAT
87495 TGTGTTATTA
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
21 14 0.41
22 2 0.06
23 2 0.06
24 4 0.12
25 12 0.35
ACGTcount: A:0.45, C:0.10, G:0.10, T:0.35
Consensus pattern (22 bp):
ATTATCAAAATTTCATAGGAAA
Found at i:87549 original size:22 final size:22
Alignment explanation
Indices: 87478--87649 Score: 84
Period size: 22 Copynumber: 7.8 Consensus size: 22
87468 TTTATAGGAA
**
87478 GATTATCAAAATTTCATTGTGT
1 GATTATCAAAATTTCATAATGT
* *
87500 TATTATCAAATTTTCA-AA-GT
1 GATTATCAAAATTTCATAATGT
*
87520 GAGGTTATCAAAATTACATAATGT
1 GA--TTATCAAAATTTCATAATGT
** *
87544 GATTATCGGAATTTCATAGA-GG
1 GATTATCAAAATTTCATA-ATGT
* * * ***
87566 GGTCGA-CAAAATTTTATAAAAA
1 GAT-TATCAAAATTTCATAATGT
* ***
87588 GGTTATCAAAATTTCATAAAAA
1 GATTATCAAAATTTCATAATGT
* *
87610 GATTATCAAATTTTCAAAATGT
1 GATTATCAAAATTTCATAATGT
87632 GATTA-CAAAAATTTCATA
1 GATTATC-AAAATTTCATA
87650 GTGGTATTTA
Statistics
Matches: 113, Mismatches: 28, Indels: 18
0.71 0.18 0.11
Matches are distributed among these distances:
20 3 0.03
21 3 0.03
22 99 0.88
23 4 0.04
24 4 0.04
ACGTcount: A:0.42, C:0.09, G:0.13, T:0.36
Consensus pattern (22 bp):
GATTATCAAAATTTCATAATGT
Found at i:87756 original size:20 final size:20
Alignment explanation
Indices: 87731--87804 Score: 103
Period size: 20 Copynumber: 3.6 Consensus size: 20
87721 TTATTGAGTA
87731 ATCAAAATTTCAGAGAGGAT
1 ATCAAAATTTCAGAGAGGAT
*
87751 ATCAAAATTTCAGGGAGGAT
1 ATCAAAATTTCAGAGAGGAT
* *
87771 ATCAAAATTTCATATGAAGGTT
1 ATCAAAATTTCAGA-G-AGGAT
87793 ATCAAAATTTCA
1 ATCAAAATTTCA
87805 TAGTTTAGTT
Statistics
Matches: 48, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
20 31 0.65
21 1 0.02
22 16 0.33
ACGTcount: A:0.43, C:0.11, G:0.16, T:0.30
Consensus pattern (20 bp):
ATCAAAATTTCAGAGAGGAT
Found at i:87798 original size:22 final size:22
Alignment explanation
Indices: 87731--88305 Score: 168
Period size: 22 Copynumber: 26.6 Consensus size: 22
87721 TTATTGAGTA
* *
87731 ATCAAAATTTCAGA-G-AGGAT
1 ATCAAAATTTCATATGAAGGTT
* * *
87751 ATCAAAATTTC--AGGGAGGAT
1 ATCAAAATTTCATATGAAGGTT
87771 ATCAAAATTTCATATGAAGGTT
1 ATCAAAATTTCATATGAAGGTT
**
87793 ATCAAAATTTCATAGTTTA-GTT
1 ATCAAAATTTCATA-TGAAGGTT
* * *
87815 TTCAAAATTTCATAAGAGGGTT
1 ATCAAAATTTCATATGAAGGTT
* * *
87837 ATCAAAATTTCATA-GTATGTAG
1 ATCAAAATTTCATATGAAGGT-T
* *
87859 ATCAAAATTTCACT-GGAAGATT
1 ATCAAAATTTCA-TATGAAGGTT
*
87881 AACAAAATTTCATAATG-AGGTT
1 ATCAAAATTTCAT-ATGAAGGTT
** * *
87903 ATCAAAAAATCATAGGGAGGTT
1 ATCAAAATTTCATATGAAGGTT
* *
87925 AT-AAAA---C-TTTG--TGTT
1 ATCAAAATTTCATATGAAGGTT
* * *
87940 ATCAAGATTTCATAAGAAAGTT
1 ATCAAAATTTCATATGAAGGTT
* * *
87962 ATCAAAATTTTATAGGGAGGTTT
1 ATCAAAATTTCATATGAAGG-TT
* **
87985 ATCAAAATTT-ATAAGAAAATTT
1 ATCAAAATTTCATATG-AAGGTT
*
88007 ATCAAAATTTCATAGCGAA-GTT
1 ATCAAAATTTCATA-TGAAGGTT
* * *
88029 ATCACAATTTCATAGTG-TGATT
1 ATCAAAATTTCATA-TGAAGGTT
*
88051 A-CGAACAATTT-ATATGGAGGTT
1 ATC-AA-AATTTCATATGAAGGTT
* * * * *
88073 TTTAAATTTTCATAACG-TGGTT
1 ATCAAAATTTCAT-ATGAAGGTT
*
88095 AT-AAATATATCATAT-AGAGGTT
1 ATCAAA-ATTTCATATGA-AGGTT
* * **
88117 ATCAACATCTCATAGTGTTGGTT
1 ATCAAAATTTCATA-TGAAGGTT
*
88140 ATCAAAATTTTAT-TGGGAA-GTT
1 ATCAAAATTTCATAT--GAAGGTT
88162 ATCAAAATTTCATATTG-AGGTGT
1 ATCAAAATTTCATA-TGAAGGT-T
* * * *
88185 -TCAAAATTACTTAAGGAGGTT
1 ATCAAAATTTCATATGAAGGTT
* * *
88206 AACAAAATTTGATAAGAAGGTT
1 ATCAAAATTTCATATGAAGGTT
* **
88228 A--AAATAATT-ATAAAAAGGTT
1 ATCAAA-ATTTCATATGAAGGTT
* * * ***
88248 TTCGAAATTCCATA-GTATCATT
1 ATCAAAATTTCATATG-AAGGTT
* *
88270 ATTAAAATTTCATAGGAAGGTT
1 ATCAAAATTTCATATGAAGGTT
88292 ATCAAAATTTCATA
1 ATCAAAATTTCATA
88306 AGGAGATCAT
Statistics
Matches: 408, Mismatches: 97, Indels: 98
0.68 0.16 0.16
Matches are distributed among these distances:
15 5 0.01
16 3 0.01
17 2 0.00
18 2 0.00
19 2 0.00
20 42 0.10
21 30 0.07
22 268 0.66
23 52 0.13
24 2 0.00
ACGTcount: A:0.40, C:0.09, G:0.15, T:0.35
Consensus pattern (22 bp):
ATCAAAATTTCATATGAAGGTT
Found at i:88009 original size:45 final size:44
Alignment explanation
Indices: 87937--88042 Score: 133
Period size: 45 Copynumber: 2.4 Consensus size: 44
87927 AAAACTTTGT
* * * *
87937 GTTATCAAGATTTCATAAGAAAGTTATCAAAATTTTATAGGGAG
1 GTTATCAAAATTTCATAAGAAAGTTATCAAAATTTCATAGCGAA
*
87981 GTTTATCAAAATTT-ATAAGAAAATTTATCAAAATTTCATAGCGAA
1 G-TTATCAAAATTTCATAAG-AAAGTTATCAAAATTTCATAGCGAA
*
88026 GTTATCACAATTTCATA
1 GTTATCAAAATTTCATA
88043 GTGTGATTAC
Statistics
Matches: 53, Mismatches: 6, Indels: 5
0.83 0.09 0.08
Matches are distributed among these distances:
44 17 0.32
45 36 0.68
ACGTcount: A:0.42, C:0.09, G:0.12, T:0.36
Consensus pattern (44 bp):
GTTATCAAAATTTCATAAGAAAGTTATCAAAATTTCATAGCGAA
Found at i:88320 original size:22 final size:22
Alignment explanation
Indices: 88273--88320 Score: 53
Period size: 22 Copynumber: 2.2 Consensus size: 22
88263 TATCATTATT
* * *
88273 AAAATTTCATAGGAAGGTTATC
1 AAAATTTCATAGGAAGATCATA
88295 AAAATTTCATAAGG-AGATCATA
1 AAAATTTCAT-AGGAAGATCATA
88317 AAAA
1 AAAA
88321 ATAGTGTAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
22 19 0.86
23 3 0.14
ACGTcount: A:0.50, C:0.08, G:0.15, T:0.27
Consensus pattern (22 bp):
AAAATTTCATAGGAAGATCATA
Found at i:91182 original size:20 final size:20
Alignment explanation
Indices: 91140--91182 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
91130 TGAGGAGGGG
* *
91140 AAAGAGGAGATGAAAAAACA
1 AAAGAGGAAAAGAAAAAACA
91160 AAAGAGGAAAAGAAGAAAA-A
1 AAAGAGGAAAAGAA-AAAACA
91180 AAA
1 AAA
91183 ATTTAAAAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 16 0.80
21 4 0.20
ACGTcount: A:0.72, C:0.02, G:0.23, T:0.02
Consensus pattern (20 bp):
AAAGAGGAAAAGAAAAAACA
Found at i:92206 original size:20 final size:19
Alignment explanation
Indices: 92178--92219 Score: 57
Period size: 20 Copynumber: 2.2 Consensus size: 19
92168 CAAGCAGGGA
*
92178 AGAGGCTCTCATGTAGAGAG
1 AGAGACTCTCATGTA-AGAG
*
92198 AGAGACTCTCATTTAAGAG
1 AGAGACTCTCATGTAAGAG
92217 AGA
1 AGA
92220 AAAAGTAGAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 7 0.35
20 13 0.65
ACGTcount: A:0.36, C:0.14, G:0.29, T:0.21
Consensus pattern (19 bp):
AGAGACTCTCATGTAAGAG
Found at i:92793 original size:24 final size:24
Alignment explanation
Indices: 92766--92815 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
92756 GCCTATAATA
*
92766 TAAATAGTGGCGTCTA-GACGCTGC
1 TAAATAGTGGCATC-AGGACGCTGC
92790 TAAATAGTGGCATCAGGACGCTGC
1 TAAATAGTGGCATCAGGACGCTGC
92814 TA
1 TA
92816 TATGCAAATT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
23 1 0.04
24 23 0.96
ACGTcount: A:0.28, C:0.20, G:0.28, T:0.24
Consensus pattern (24 bp):
TAAATAGTGGCATCAGGACGCTGC
Found at i:93755 original size:20 final size:21
Alignment explanation
Indices: 93720--93761 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
93710 TACTCGTGTC
93720 AAGACACGACTAACACG-TTT
1 AAGACACGACTAACACGCTTT
* *
93740 AAGACACGAGTGACACGCTTT
1 AAGACACGACTAACACGCTTT
93761 A
1 A
93762 TTTAACGGGT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 15 0.79
21 4 0.21
ACGTcount: A:0.38, C:0.24, G:0.19, T:0.19
Consensus pattern (21 bp):
AAGACACGACTAACACGCTTT
Found at i:94288 original size:17 final size:17
Alignment explanation
Indices: 94266--94304 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
94256 CCTAATAATT
*
94266 AAAATTGAAATAAAATA
1 AAAATTAAAATAAAATA
*
94283 AAAATTAAAATAAATTA
1 AAAATTAAAATAAAATA
94300 AAAAT
1 AAAAT
94305 ATCAATAACT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.72, C:0.00, G:0.03, T:0.26
Consensus pattern (17 bp):
AAAATTAAAATAAAATA
Found at i:98836 original size:18 final size:18
Alignment explanation
Indices: 98813--98851 Score: 53
Period size: 19 Copynumber: 2.2 Consensus size: 18
98803 CTCATCAAAG
98813 GAAG-AAATCAAAATAACA
1 GAAGAAAATCAAAATAA-A
*
98831 GAAGAAAATCAGAATAAA
1 GAAGAAAATCAAAATAAA
98849 GAA
1 GAA
98852 ATGAAGTCTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 8 0.42
19 11 0.58
ACGTcount: A:0.67, C:0.08, G:0.15, T:0.10
Consensus pattern (18 bp):
GAAGAAAATCAAAATAAA
Found at i:103444 original size:13 final size:13
Alignment explanation
Indices: 103426--103450 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
103416 TTAGTTTGGA
103426 AGAAGTGCTTTTG
1 AGAAGTGCTTTTG
103439 AGAAGTGCTTTT
1 AGAAGTGCTTTT
103451 TTAAATTGCG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.24, C:0.08, G:0.28, T:0.40
Consensus pattern (13 bp):
AGAAGTGCTTTTG
Found at i:107001 original size:65 final size:65
Alignment explanation
Indices: 106896--107024 Score: 213
Period size: 65 Copynumber: 2.0 Consensus size: 65
106886 CAATCCAGAG
* * * *
106896 TCATAAAACTACTATCTCCTCCTTGATTTGTTAAGTAGTCTCAATTGAGTAACAGAGTAACAAAA
1 TCATAAAACTACTATCTACTCCTTGATTTGTTAAGCAGTCTCAATTAACTAACAGAGTAACAAAA
*
106961 TCATAAAACTACTGTCTACTCCTTGATTTGTTAAGCAGTCTCAATTAACTAACAGAGTAACAAA
1 TCATAAAACTACTATCTACTCCTTGATTTGTTAAGCAGTCTCAATTAACTAACAGAGTAACAAA
107025 TTAAGCTAAC
Statistics
Matches: 59, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
65 59 1.00
ACGTcount: A:0.37, C:0.19, G:0.12, T:0.32
Consensus pattern (65 bp):
TCATAAAACTACTATCTACTCCTTGATTTGTTAAGCAGTCTCAATTAACTAACAGAGTAACAAAA
Found at i:113241 original size:87 final size:89
Alignment explanation
Indices: 113090--113250 Score: 283
Period size: 87 Copynumber: 1.8 Consensus size: 89
113080 GGAAATACTC
113090 GGGAACCCTAGGTCGATGATAAAAAAAAGGAATTTAAATAGGAGAAAACAATGATAAAGAGAAAA
1 GGGAACCCTAGGTCGATGATAAAAAAAAGGAATTTAAATAGGAGAAAACAATGATAAAGAGAAAA
113155 GATTGAAATTATATGGAAATAAAA
66 GATTGAAATTATATGGAAATAAAA
*
113179 GGGAACCCTAGGTCGAT-A-AAAAGAAAAGGAATTTAAAT-GGAGAAAACAATGATGAAGAGAAA
1 GGGAACCCTAGGTCGATGATAAAA-AAAAGGAATTTAAATAGGAGAAAACAATGATAAAGAGAAA
113241 AGATTGAAAT
65 AGATTGAAAT
113251 CCTATAAAAA
Statistics
Matches: 70, Mismatches: 1, Indels: 4
0.93 0.01 0.05
Matches are distributed among these distances:
87 37 0.53
88 16 0.23
89 17 0.24
ACGTcount: A:0.53, C:0.06, G:0.23, T:0.18
Consensus pattern (89 bp):
GGGAACCCTAGGTCGATGATAAAAAAAAGGAATTTAAATAGGAGAAAACAATGATAAAGAGAAAA
GATTGAAATTATATGGAAATAAAA
Found at i:115916 original size:3 final size:3
Alignment explanation
Indices: 115908--115939 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
115898 TTTTTATTTA
115908 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
115940 GGCCTGTCTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:119460 original size:13 final size:13
Alignment explanation
Indices: 119442--119466 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
119432 GAATACTAAA
119442 ATTTCTATTCTAT
1 ATTTCTATTCTAT
119455 ATTTCTATTCTA
1 ATTTCTATTCTA
119467 CTTGATGCAG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.24, C:0.16, G:0.00, T:0.60
Consensus pattern (13 bp):
ATTTCTATTCTAT
Found at i:121221 original size:12 final size:12
Alignment explanation
Indices: 121204--121228 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
121194 TATAACATGT
121204 TGTTTTGTTCTG
1 TGTTTTGTTCTG
121216 TGTTTTGTTCTG
1 TGTTTTGTTCTG
121228 T
1 T
121229 TTGTGCAGTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.08, G:0.24, T:0.68
Consensus pattern (12 bp):
TGTTTTGTTCTG
Found at i:126740 original size:28 final size:28
Alignment explanation
Indices: 126685--126743 Score: 75
Period size: 29 Copynumber: 2.1 Consensus size: 28
126675 GGCCAATACT
* **
126685 TAACCCCTAATCATCCAAGGATGTATCC
1 TAACCCCTAATCATCCAAGCATAAATCC
126713 TAACCGCCTAATCATCCAAGCA-AAATCC
1 TAACC-CCTAATCATCCAAGCATAAATCC
126741 TAA
1 TAA
126744 TATTAGAACT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
28 12 0.44
29 15 0.56
ACGTcount: A:0.37, C:0.32, G:0.08, T:0.22
Consensus pattern (28 bp):
TAACCCCTAATCATCCAAGCATAAATCC
Found at i:130096 original size:25 final size:24
Alignment explanation
Indices: 130050--130097 Score: 60
Period size: 25 Copynumber: 2.0 Consensus size: 24
130040 TGGGCTTGGC
*
130050 ACTTTGGTGATCGATTAATGAGAG
1 ACTTTGATGATCGATTAATGAGAG
* *
130074 ACTTTGATGCATCTATTATTGAGA
1 ACTTTGATG-ATCGATTAATGAGA
130098 TTTGGGGGCT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 8 0.40
25 12 0.60
ACGTcount: A:0.29, C:0.10, G:0.23, T:0.38
Consensus pattern (24 bp):
ACTTTGATGATCGATTAATGAGAG
Found at i:133727 original size:2 final size:2
Alignment explanation
Indices: 133720--133749 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
133710 GAGTAATTGA
133720 AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
133750 ATTCAACACC
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.